Analysis Overview for Kidney Renal Clear Cell Carcinoma
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Overview
Introduction

This is the analysis overview for Firehose run "21 December 2012".

Summary

Note: These results are offered to the community as an additional reference point, enabling a wide range of cancer biologists, clinical investigators, and genome and computational scientists to easily incorporate TCGA into the backdrop of ongoing research. While every effort is made to ensure that Firehose input data and algorithms are of the highest possible quality, these analyses have not been reviewed by domain experts.

Results

  • Sequence and Copy Number Analyses

    • Copy number analysis (GISTIC2)
      View Report | There were 493 tumor samples used in this analysis: 28 significant arm-level results, 12 significant focal amplifications, and 18 significant focal deletions were found.

    • Mutation Analysis (MutSig v2.0)
      View Report | 

    • Mutation Analysis (MutSig vS2N)
      View Report | 

  • Clustering Analyses

    • Clustering of copy number data: consensus NMF
      View Report | The most robust consensus NMF clustering of 493 samples using the 30 copy number focal regions was identified for k = 3 clusters. We computed the clustering for k = 2 to k = 8 and used the cophenetic correlation coefficient to determine the best solution.

    • Clustering of Methylation: consensus NMF
      View Report | The 2001 most variable methylated genes were selected based on variation. The variation cutoff are set for each tumor type empirically by fitting a bimodal distriution. For genes with multiple methylation probes, we chose the most variable one to represent the gene. Consensus NMF clustering of 283 samples and 2001 genes identified 3 subtypes with the stability of the clustering increasing for k = 2 to k = 8 and the average silhouette width calculation for selecting the robust clusters.

    • Clustering of RPPA data: consensus NMF
      View Report | The most robust consensus NMF clustering of 454 samples using the 150 most variable proteins was identified for k = 3 clusters. We computed the clustering for k = 2 to k = 8 and used the cophenetic correlation coefficient to determine the best solution.

    • Clustering of RPPA data: consensus hierarchical
      View Report | The 150 most variable proteins were selected. Consensus average linkage hierarchical clustering of 454 samples and 150 proteins identified 3 subtypes with the stability of the clustering increasing for k = 2 to k = 8 and the average silhouette width calculation for selecting the robust clusters.

    • Clustering of mRNA expression: consensus NMF
      View Report | The most robust consensus NMF clustering of 72 samples using the 1500 most variable genes was identified for k = 3 clusters. We computed the clustering for k = 2 to k = 8 and used the cophenetic correlation coefficient to determine the best solution.

    • Clustering of mRNA expression: consensus hierarchical
      View Report | The 1500 most variable genes were selected. Consensus average linkage hierarchical clustering of 72 samples and 1500 genes identified 3 subtypes with the stability of the clustering increasing for k = 2 to k = 8 and the average silhouette width calculation for selecting the robust clusters.

    • Clustering of mRNAseq gene expression: consensus NMF
      View Report | The most robust consensus NMF clustering of 469 samples using the 1500 most variable genes was identified for k = 3 clusters. We computed the clustering for k = 2 to k = 8 and used the cophenetic correlation coefficient to determine the best solution.

    • Clustering of mRNAseq gene expression: consensus hierarchical
      View Report | The 1500 most variable genes were selected. Consensus average linkage hierarchical clustering of 469 samples and 1500 genes identified 3 subtypes with the stability of the clustering increasing for k = 2 to k = 8 and the average silhouette width calculation for selecting the robust clusters.

    • Clustering of miRseq expression: consensus NMF
      View Report | We filtered the data to 150 most variable miRs. Consensus NMF clustering of 480 samples and 150 miRs identified 3 subtypes with the stability of the clustering increasing for k = 2 to k = 8 and the average silhouette width calculation for selecting the robust clusters.

    • Clustering of miRseq expression: consensus hierarchical
      View Report | We filtered the data to 150 most variable miRs. Consensus average linkage hierarchical clustering of 480 samples and 150 miRs identified 3 subtypes with the stability of the clustering increasing for k = 2 to k = 8 and the average silhouette width calculation for selecting the robust clusters.

  • Correlation Analyses

    • Correlation between copy number variations of arm-level result and selected clinical features
      View Report | Testing the association between copy number variation 71 arm-level results and 8 clinical features across 493 patients, 3 significant findings detected with Q value < 0.25.

    • Correlation between copy number variation genes and selected clinical features
      View Report | Testing the association between copy number variation of 30 peak regions and 8 clinical features across 493 patients, 26 significant findings detected with Q value < 0.25.

    • Correlation between gene methylation status and clinical features
      View Report | Testing the association between 17341 genes and 8 clinical features across 263 samples, statistically thresholded by Q value < 0.05, 7 clinical features related to at least one genes.

    • Correlation between molecular cancer subtypes and selected clinical features
      View Report | Testing the association between subtypes identified by 10 different clustering approaches and 8 clinical features across 502 patients, 47 significant findings detected with P value < 0.05.

    • Correlation between gene mutation status and selected clinical features
      View Report | Testing the association between mutation status of 34 genes and 8 clinical features across 293 patients, 2 significant findings detected with Q value < 0.25.

    • Correlation between RPPA expression and clinical features
      View Report | Testing the association between 166 genes and 8 clinical features across 454 samples, statistically thresholded by Q value < 0.05, 7 clinical features related to at least one genes.

    • Correlation between mRNA expression and clinical features
      View Report | Testing the association between 17814 genes and 7 clinical features across 72 samples, statistically thresholded by Q value < 0.05, 5 clinical features related to at least one genes.

    • Correlation between mRNAseq expression and clinical features
      View Report | Testing the association between 18300 genes and 8 clinical features across 469 samples, statistically thresholded by Q value < 0.05, 7 clinical features related to at least one genes.

    • Correlation between miRseq expression and clinical features
      View Report | Testing the association between 471 genes and 8 clinical features across 480 samples, statistically thresholded by Q value < 0.05, 6 clinical features related to at least one genes.

    • Correlations between copy number and mRNA expression
      View Report | The correlation coefficients in 10, 20, 30, 40, 50, 60, 70, 80, 90 percentiles are -0.21832, -0.0867, 0.0089, 0.0926, 0.1695, 0.2409, 0.3176, 0.40086, 0.5043, respectively.

    • Correlations between copy number and mRNAseq expression
      View Report | The correlation coefficients in 10, 20, 30, 40, 50, 60, 70, 80, 90 percentiles are 720, 1609.6, 2052, 2456.2, 2890.5, 3354.8, 3885, 4471, 5221, respectively.

    • Correlation between mRNA expression and DNA methylation
      View Report | The top 25 correlated methylation probes per gene are displayed. Total number of matched samples = 263. Number of gene expression samples = 469. Number of methylation samples = 263.

  • Other Analyses

    • PARADIGM pathway analysis of mRNA expression data
      View Report | There were 70 significant pathways identified in this analysis.

    • PARADIGM pathway analysis of mRNA expression and copy number data
      View Report | There were 62 significant pathways identified in this analysis.

    • PARADIGM pathway analysis of mRNASeq expression data
      View Report | There were 42 significant pathways identified in this analysis.

    • PARADIGM pathway analysis of mRNASeq expression and copy number data
      View Report | There were 43 significant pathways identified in this analysis.

    • The boxplot mRNA array based expression data
      View Report

Methods & Data
Input

  • Run Prefix = analyses__2012_12_21

  • Summary Report Date = Fri Jan 25 11:38:16 2013

  • Protection = FALSE

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